While we tend to hear more about SIBO causing IBS, SIFO (small intestinal fungal overgrowth) is a common issue that also causes IBS-type symptoms. Discover the most common symptoms of SIFO, how to diagnose it, and how to treat SIFO.

SIBO has become a hot topic lately and is being identified as a common cause of IBS. However, SIBO may not be the only culprit. We’re now realizing that SIFO (small intestinal fungal overgrowth) is also a common issue that causes IBS-type symptoms. SIFO is a little more difficult to test for and diagnose, but it should be considered when a patient presents with symptoms of IBS and doesn’t respond to typical SIBO treatment.

Many patients exhibit symptoms of SIBO, but their breath test is negative. Or they have a positive breath test, undergo treatment, and still don’t feel better. In 2013, Dr. Satish Rao and his team published a study of 124 patients with IBS symptoms evaluated over 5 to 10 years. Researchers cultured juice from the small bowel of these patients. They found over 62% of patients had an infection in the small bowel. These are patients who are otherwise healthy. They didn’t have any other type of infection that made them sick. They just had a GI infection that was causing digestive symptoms.

As the results were broken down further, they found that 25% of the patients had SIBO, 20% of the patients had both SIBO and SIFO, and 20% had SIFO. In other words, 40% of these patients had fungal overgrowth in the small intestine.

Symptoms are very poor predictors of underlying causes because these symptoms can be related to a number of different GI conditions. However, after treatment for SIFO, people usually see a dramatic change in symptoms and feel incredibly better.

It’s been observed that non-GI symptoms also improve, such as fatigue, joint pain, energy, and headaches.

Most common symptoms of SIFO:

Belching

Bloating

Fullness

Gas

Nausea

Diarrhea

There are several reasons that we’re seeing this increased rate of SIFO in our population. A few reasons are listed below.

Reasons why SIFO is an issue:

Excessive antibiotic usage

Long-term use of proton pump inhibitors (PPIs)

Metabolic conditions like diabetes

Inflammatory bowel disease (IBD)

Dysmotility and neurological issues

Connective tissue disorders

Genetic predisposition

How to diagnose SIFO

Testing for SIFO is a more invasive process. A breath test for SIFO at this point is not an option because fungus doesn’t ferment like bacteria. Therefore, you wouldn’t be able to measure the level of fungus in the breath. Currently, the best test available to diagnose SIFO is a small bowel aspirate via endoscopy.

SIFO Testing Options

Small intestine aspirate: Taking fluid from the small bowel and aspirating it. This is the gold standard.

Stool testing: You can see Candida in stool, but this may lead to a false positive for SIFO.

Blood antibody testing: Not a perfect test, but certainly an option and much less invasive.

Blood antibody testing is an option for Candida, but there is still concern as to whether it’s an accurate test. The main concern with antibody testing is that it doesn’t tell you if you have an active infection. It simply suggests that you may have it or you previously had it at one point in your life. This may be more reliable than the stool test, but less accurate than the aspirate.

The future is very promising in regards to testing methods. Researchers are currently working on capsules that you can ingest that will sample small intestinal juice every 15 minutes to diagnose SIFO. This will be a very easy, minimally invasive method. In 2 to 3 years, we will have simple methods for testing. At this point, endoscopy is the best way to diagnose SIFO.

Alternatively, you have the option of treating based on symptoms. Doing a short round of antifungals is not likely to cause any negative problems. If the patient responds well, then you have pretty good confirmation that SIFO is an issue.

How to treat SIFO — Herbals vs. Pharmaceuticals

Herbal antimicrobials may be a great option because they are more broad-spectrum. They can treat both bacterial overgrowth and fungal overgrowth. The downside is that herbal agents usually require longer treatment duration. Herbs also have additional benefits. For example, oil of oregano has shown to have anti-depressant benefits. Berberine is effective at lowering and controlling blood sugar. Artemisinin has been shown to induce remission in IBD.

Herbs may be a little bit safer compared to a pharmaceutical antifungal. The main downsides to herbs are that they’re not covered by insurance, they require longer treatment duration, and there are more pills to take versus a pharmaceutical agent. You also have to be very careful with the quality of herbs and make sure you’re using a reputable brand. We highly recommend working with a skilled practitioner to help you determine the type and dosing of antimicrobials.

There are several pharmaceutical options that can be helpful in treating SIFO. When choosing an antifungal for SIFO, you need a compound that will stay intact to get to the small intestine. You want to make sure the stomach acid won’t break it up. Dr. Rao recommends fluconazole as an effective and safe option. He suggests taking one pill per day (100mg) for 3 weeks. If the patient doesn’t respond to this treatment, consider switching to itraconazole or posaconazole.

Nystatin is a popular antifungal agent. However, Dr. Rao is concerned with whether it is delivered to the small bowel. It may get broken down in the stomach, which wouldn’t make it a good option for SIFO. It’s a better option for oral and esophageal fungal infections.

For patients who have both SIBO and SIFO, Dr. Rao treats in the following way: For week 1, they get an antibiotic, such as rifaximin. In the second week, he uses both an antibiotic and antifungal. Then weeks 3 and 4, the patient takes just the antifungal.

For patients with recurrent SIFO and/or SIBO, Dr. Rao prefers giving cyclical antibiotics and antifungals over prokinetics. For some patients he uses both. We don’t have many great prokinetic options in the US, so he finds that cycling antibiotics and antifungals works better for his patients.

Additionally, he doesn’t use probiotics very often for his SIFO and SIBO patients because of his concern over colonizing the bacteria in the small intestine rather than the colon.

To learn more about diagnosing and treating SIFO, listen to our podcast with Dr. Satish Rao.

What do you think? I would like to hear your thoughts or experience with this.

I care about answering your questions and sharing my knowledge with you. Leave a comment or connect with me on social media asking any health question you may have and I just might incorporate it into our next listener questions podcast episode just for you!

Hi Brad,
It’s hard to say because we rarely are able to quantify SIFO via lab testing – so we are not sure if a treatment has reduced SIFO. Most clinicians use symptomatic improvements to gauge this. Dr. Rao uses Fluconazole, I use and suspect many herbals are also effective based upon my clinical observations.

Yes, I did a saliva antibody test for candida a few years ago when I was working with a practitioner. A previous stool test had shown no yeast, but the saliva antibody test came back positive on IgA (active infection) and IgG (past infection).

Thanks Ross. Interesting test, it doesn’t appear to be available in the US though. There is the potential for urine organic acids but I am not committing to this until I have a chance to perform a literature review. Hope this helps and stay tuned for review.

Hi Kelli,
It may be helpful to start with a lower carb paleo diet (very similar to a candida diet) and then perform the reintroduction to see where you feel best. One of the main variables for yeast/fungus is carb intake but there is more to finding your ideal diet than just carbs. My book will lay out a good plan for this. Ultimately the best diet for you is the one you feel best on and not what a given conditions diet rules recommend. Hope this helps!

Hello
I tested positive for Sibo and took many antimicrobial herbs then took antibiotic Rifaximin and neomycin all to no avail Now taking Diflucan in case of Sifo
Would you recommend taking Alliimed and/or berberine for Sibo while taking antibiotic for Sifo
I don’t want Sibo to get worse
I will be talking another sibo test soon

Hi Marie,
I would find a good clinician because if you are responding poorly to treatment then you will likely need someone to craft a personalized application of the available treatment options. You can contact my office if you need help, http://www.drruscio.com/gethelp or wait for my book for a self help approach, http://www.drruscio.com/gutbook.
Hope this helps!

I have tested positive for SIBO(via saliva test) and scant fungal overgrowth(via a stool test). It would be best Tovah treat both, yes? It would be difficult to know what is causing the issues.
I do have issues with motility. I know it’s important to treat the underlying infections, but is poor motility the route of the problem here? And correcting that needs to be addressed?

Sue,
I would seriously question a saliva test for SIBO, be careful here. There is no short answer here. If you can’t find a good clinician to help you then I would go through the self help plan in my coming print book, http://www.drruscio.com/GutBook.
Hope this helps!

Hi!
I found that herbal antibiotics, candida enzymes, low FODMAP diet and enemas keep things at bay, but when consuming prebiotic foods (like in a green superfood powder) aggravate my digestive system. What am I missing? Digestive enzymes/HCL/DAO? oh, and staying away from histamine foods too.
Any suggestions? What prokinetics would you suggest besides ginger? I found that laxative teas relieve discomfort almost within an hour, which makes me suspect SIBO/SIFO but clearly not something I consider as a solution. Also, since daily enemas, there has been no need for such tea.
Thank you!

While I understand why taking probiotics might be problematic for individuals dealing with SIBO and/or SIFO, does this change when a patient’s stool test indicates no growth at all of beneficial bacteria, for example bifidobacterium? If a lack of beneficial bacteria is causing other major symptoms in the individual, but they also have SIBO/SIFO, should they just treat the SIBO/SIFO and ignore the missing bifido? It seems like these types of patients can’t do anything in either direction. What’s worse, the risk of symptoms from not managing the dysbiosis out of fear of aggravating SIBO/SIFO or the risk of causing further SIBO from attempting to address the dysbiosis? Thanks.

Good question Jay. Some people experience temporary oral thrush while on ED, which clears quickly when coming off. In terms of intestinal fungus, I think it could go either way depending on the person. This is where the home made lower carb version of the ED may be helpful, for those who are carb sensitive.

I had bad constipation vs diarrhea. Yet am convinced that I have/had SIFO. Can constipation be a symptom of SIFO, too? Recently tho, after a week long dose of Diflucan for another fungal issue (a skin fungal rash called Tinea Versicolor) and for toenail fungus, my health has greatly improved!

Is alcohol intolerance a possible symptom / byproduct of SIFO? I cannot tolerate alcohol anymore (nausea and diarrhea starting hours after I’ve had just 1/2 of a drink and hangover symptoms the entire next day). I was diagnosed with methane SIBO but my tolerance did not return after I cleared the SIBO..

Hi Shannon – no, have not found any reasons or treatment unfortunately. The only thing I found after extensive searching online was that a handful of people reporting sudden alcohol intolerance online ended up testing positive for SIBO. I did test positive for SIBO myself, but after clearing it, I still did not regain my tolerance. It did make me *slightly* better — instead of a few sips making me feel terrible almost right away, I can now drink 1/2 a drink. I will still feel terrible, but it’s hours later instead of right away. Perhaps my gut never healed enough? It’s frustrating…

I also have intense intolerance and SIBO for years and likely SIFO since I’ve had relief of smell sensitivities post-antifungal treatment. Cannot rid the symptoms. Is there a pod cast that goes over this alcohol intolerance question?

Hey, I have noticed that too. I’ve never been a big drinker, and even before I had severe stomach issues, I had trouble with red wine upsetting my stomach and causing reflux (I have been told it’s the sulfites?) but I was for the most part, able to tolerate most anything else (I am not big on beer, but I have tried to sip one since this started and even 1/2 a bottle bothers me). I can mostly tolerate clear liquors, and white wines, but I can only tolerate maybe 1-3 drinks. Even at that, it usually gives me reflux and on occasion a bad flare with horrible burps (smells like sulfur, was told by an acquaintance this is sour stomach), and my emergency meds do little. If the burping gets bad enough it will make me nauseous and occasionally vomit. However I rarely feel the brunt of the effects when I’m still consuming the alcohol or later that day/night. It’s the next day and possibly a few days after that my stomach really gets going.

Also before developing the stomach problems, I very rarely got a hang over, and at least that part hasn’t changed. Although a couple of years ago I had one and I hadn’t really had a lot to drink, but the hangover was the worst of my entire life, and I don’t really understand why. I only had two drinks of sparkling white wine, a glass 0f tea with dinner, and I had been drinking water most of the day, and continued to do so while drinking and afterward.

I have found one of the easiest things for my stomach (it’s almost ironic really) has been clear tequila. unlike the brown/gold it doesn’t upset my stomach, and as long as I’m not consuming a huge margarita, it doesn’t give me reflux.

However I mainly started turning to it because whatever is wrong with my stomach (I have been diagnosed IBS-D, but I was urged by a friend to find a new doctor, as my current GI is more incompetent than I realized. But it’s a strong possibility I have Crohn’s instead), also came hand-in-hand with severe weight gain (I know, that’s usually the opposite of what IBD patients experience. Idk why I just know when I flare I gain, and when I’m not flaring, I’m starting to actually lose weight again. For a long time I was gaining but couldn’t lose to save my life.

And I was reading about things that help with weight/diet, and also blood sugar (I’m not diabetic but I’m at risk and my blood sugar seems to be unstable) and I found out tequila (clear only I think, but I’m not sure) has a low glycemic index so it doesn’t cause a blood sugar spike.

I would say check into possibly healing your gut more before drinking again, but if you absolutely want to have something to drink, you might try my method and see if that helps you. Another thing I have noticed is I seem to be intolerant to lots of added sugar, so if you do choose this method, be careful with sweet wines (although a local winery by me makes honey wine, and it is so, so good), and with liquors, be careful with oversweetened mixers.

For example, I was making a slimmed down version of a margarita by using scant amounts of honey or agave, fresh lime juice, and a splash of fresh orange and lemon juice, and water to taste. I tried doing a frozen version, but it’s hard to get the ice ratio right. if you are going to do this I would suggest omitting water from the drink, or preparing the mixer ahead of time and freezing it to make frozen margaritas. However, for a no-fuss easy to mix drink, I prefer to make it on the rocks. I’m big on the salted rim too, and I think it helps to balance out the bitterness of the barely sweet mixer.

Hi Dr. Ruscio,
I have SIBO-C and both my naturopath and I suspect I also have SIFO. To treat both simultaneously, do you suggest “feeding” the bacteria with high FODMAP foods during treatment? Also, do you think the strain(s) of yeast determines choice of herbs, or does it not matter? Thanks, and thanks for all your work!

My teenager has been treated for SIBO with antibiotics and herbals multiple times over the past two years but cannot seem to get rid of the SIBO completely (although the hydrogen levels reduced and methane went all the way down). Strangely, she would feel better in the beginning of treatment, go through die off, feel better, then at the end of treatment just start feeling yucky and become constipated again. I am now convinced she has SIFO as well and we are working with another doctor and are currently waiting on Blood, stool and acids test results. What are some SIFO specific herbs that you find effective. We did two rounds of Candibactin AR/BR and one month of Berberine, Neem, Allimax, along with motilpro and megasporbiotic. The megasporbiotic did amazing things for her skin. Any thoughts you have would be helpful. We tried to get in to see you but the wait is just too long. Thanks.

I like to test for SIFO but both my PCP and GI doctor said they don’t know anything about SIFO testing. Please advise me where I can take SIFO test to treat my on going issues with my gut.
Thanks,
A.S.

I was diagnosed with celiac disease 4 years ago. I don’t have symptoms relating to that since I am very careful about what I eat but I have been having other symptoms for a while now. I have borderline high cholesterol for 2 years which I’ve never had before accompanied by diarrhea after eating a lot of different foods and it seems to be growing in scope. A lot of the foods I can’t tolerate are oils and fats like peanut butter but also some gf Panko, garlic and onions, tomato sauce, spinach, carrots and others. It seems like my body can’t break it down. The fodmap diet isn’t beneficial for me since some things work and others don’t. Is it possible I have SIBO and/or SIFO? My GI doc said I probably have IBS but I do eat a diet high in carbs and sugar. I’m concerned about my cholesterol and need to get this in check since I’d like to start a family soon but I can’t figure out why my body can’t process it. I’d really appreciate any advice.

Hi Becky,
I would strongly recommend going through the protocol in Healthy Gut, Healthy You. Yes, you may have SIBO, SIFO and/or IBS – the protocol works well for all. Make sure to keep you doctor in the loop also.

Dear Dr Ruscio,
I’ve been scripted Fluconazole for ongoing vulval dermatitis. Co-incidentally I am on a low FODMAP diet due to intestinal issues (for last 4 weeks). Will the medication counter-act the positive effects of the diet. Is it okay to follow both treatments at the same time.
Many thanks
Sue

Hi Dr. Ruscio,
How do you feel about Microbial Organic Acid Testing for fungal overgrowth? (I like The Great Plains Lab better than Genova for this test) I have had 5 Genova Stool tests over the past 25 years and they all have been negative for fungus. However, I have had 4 MOAT tests over the same time period that have all been positive for fungal metabolites. I have read that these conflicting test results indicate an overgrowth in the upper GI tract, SIFO possibly? I have responded in the to fungal medications in the past, but symptoms eventually return. Now when I try treatment, both herbal or pharmacological I get an unbearable die off reaction. Your thoughts?

Hi Dr. Ruscio,
My husband and I discovered a large variety and quantity of mold in our A/C unit three years ago! Even after remediation and purchasing a vacation home, we have suffered tremendous health issues! We have spent thousands in MD’s and holistic health care!
About two years ago, I was showering with a new facial wash! For extra cleanliness I used it under my armpits and buttocks area! To my horror, I discovered these little white, rice looking things! I have had three bowel movements tests! The first just came back with no parasites and no ecoli! Last week, a new test revealed no good bacteria, no parasites, but an extreme overgrowth of what appears to be yeast but not candida ablicans! I wish I could have been tested for aspergilles or mycotoxins, but there may not be such a test! My health practitioner has me on many supplements, but my stomach was so painful, I had to go to the gastro! Again, a BM test showed negative and no parasites! Ugh! She wants me to take Xifaxan for two weeks! I have heard antibiotics can only make mold worse! However, being a flight attendant, I just want to get well! Help!